Kennerly was born at the family estate in White Post, Virginia. He attended Dickinson College in Carlisle, Pennsylvania, where Spencer F. Baird was Professor of Natural History and Curator of the Museum. After graduating from Dickinson in 1849, he studied medicine at the University of Pennsylvania, receiving his M.D. degree in 1852. Because of his early association with Baird and his involvement in government expeditions, he contributed greatly to collection building at the Smithsonian. Unfortunately, his productive life was cut short at the age of 32. He died at sea on his way back from the Northwestern Boundary Survey in February 1861, when his ship was sailing off the coast of Cape San Lucas, Baja California. Spencer Baird eulogized him in the Smithsonian Annual Report (1861):

No one of the gentlemen who have labored so zealously to extend a knowledge of the natural history of the west within the last ten or twelve years has been more successful than Dr. Kennerly. Many new species have been first described by himself or from his collections, while his contributions to the biography of American animals have been of the highest interest.

The Smithsonian Ichthyology collection includes many specimens obtained by Dr. Kennerly, and Dr. Charles Girard and Dr. George Suckley published papers describing these fishes. Girard named a sucker, a new species of fish first collected in Texas, for Kennerly (Moxostoma kennerlii) in 1856. Another new species, a salmon, (Salmo kennerlyi), was described by Suckley in 1861. Kennerly's diary (June 1853-April 1854), kept during the Pacific Railroad Survey (Whipple's Explorations along the 35th Parallel), is on deposit at the Library of Congress. During the expeditions, especially the Northwest Boundary Survey, Kennerly kept in touch with Baird by writing often from the camps where he was stationed. The Baird-Kennerly correspondence spans a twelve-year period, from 1849 to 1861, and is preserved at the Smithsonian Archives. Kennerly's report on the zoology of the expedition is found in Volume 4 of the multi-volume Reports of explorations and surveys, to ascertain the most practicable and economical route for a railroad from the Mississippi River to the Pacific Ocean, issued in 1855-1860 by the Pacific Railroad Surveys of the War Department.